Details of this dataset

Gambia_Indie-MH, 4 plates prepped between 2023_03 & 2023_04

Import data

Sample size, loci BEFORE cleanup

Explore data structure

## [1] "Sample size = 346"
## [1] "Loci = 244"
## [1] "1 to 130 alleles per locus per sample"

Merging data (TBD)

Combine multiple sequencing runs

Combine read coverage with parasite density

Adding plate map

Track input reads to amplicon

Looks at dimers

grey = input, colored = amplicons

## [1] "Overall % dimers (already multiplied x100)"
## [1] 0.5306955

Negative controls

Do neg ctrls have a lot of reads?

If so, how will you filter them?

## [1] "Max number of reads in a locus"
## [1] 344
## [1] "List of loci with >100 reads (summed over all negative controls)"
## # A tibble: 25 × 5
##    locus                         reads pool  Gene          Reason_to_include
##    <chr>                         <int> <chr> <chr>         <chr>            
##  1 Pf3D7_13_v3-2814583-2814832-2   344 2     EBL-1         HRP3 deletion    
##  2 Pf3D7_11_v3-1902041-1902278-2   290 2     MAEBL         ch11             
##  3 Pf3D7_13_v3-1726174-1726408-2   269 2     k13           <NA>             
##  4 Pf3D7_12_v3-2092654-2092884-2   249 2     coronin       100              
##  5 Pf3D7_13_v3-1725124-1725365-2   195 2     k13           613              
##  6 Pf3D7_13_v3-1725887-1726123-2   176 2     k13           <NA>             
##  7 Pf3D7_13_v3-2770591-2770863-2   170 2     PF3D7_1369500 HRP3 deletion    
##  8 Pf3D7_11_v3-1950431-1950680-2   169 2     Pf332         ch11             
##  9 Pf3D7_14_v3-294503-294768-2     160 2     pm2           cnv              
## 10 Pf3D7_03_v3-221295-221532-2     159 2     csp           C-terminal       
## # ℹ 15 more rows

Positive controls

Using a known parasite strain at a known density

Alleles should be known, and monoclonal

## [1] "Mean of total locus = 214, Mean prop. of monoclonal loci = 0.85, Mean prop. of polyclonal loci = 0.15"

Look at total amplification

All pools combined

## 
##  1A 1AB  1B 1B2   2 
## 165   5  75   2  29

Species check

Should be Pfal, and not other species

These loci will be filtered out downstream (loci 1AB)

Look at how each individual pool amplified

Pool 1A

## [1] "No reads in any samples for these loci, for 1A"
## # A tibble: 0 × 3
## # ℹ 3 variables: locus <chr>, pool <chr>, n <dbl>
## [1] "List of samples that do not have >75% loci with >100 reads, in pool 1A"
## # A tibble: 172 × 7
## # Groups:   sampleID [172]
##    sampleID                        pool  totreads   n50  n100 neg_control   norm
##    <chr>                           <chr>    <int> <int> <int> <lgl>        <dbl>
##  1 Gambia_Indie-1B_MH_1_AE_2023_0… 1A         235     0     0 FALSE       0     
##  2 Gambia_Indie-1B_MH_1_AE_2023_0… 1A        1989     4     0 FALSE       0     
##  3 Gambia_Indie-1B_MH_1_AE_2023_0… 1A        8057    61    18 FALSE       0.112 
##  4 Gambia_Indie-1B_MH_1_AE_2023_0… 1A         464     0     0 FALSE       0     
##  5 Gambia_Indie-1B_MH_1_AE_2023_0… 1A         989     0     0 FALSE       0     
##  6 Gambia_Indie-1B_MH_1_AE_2023_0… 1A        2786     7     0 FALSE       0     
##  7 Gambia_Indie-1B_MH_1_AE_2023_0… 1A        4984    28     6 FALSE       0.0375
##  8 Gambia_Indie-1B_MH_1_AE_2023_0… 1A        7523    63    16 FALSE       0.1   
##  9 Gambia_Indie-1B_MH_1_AE_2023_0… 1A        9277    77    23 FALSE       0.144 
## 10 Gambia_Indie-1B_MH_1_AE_2023_0… 1A         698     0     0 FALSE       0     
## # ℹ 162 more rows

Pool 5

## 
## TRUE 
##   47

## [1] "Loci without any reads, pool 5"
## # A tibble: 0 × 16
## # ℹ 16 variables: locus-pool <chr>, Category <chr>, chr_malaria <chr>,
## #   ampInsert_start <dbl>, ampInsert_end <dbl>, GeneID <chr>, Gene <chr>,
## #   Reason_to_include_(if_drug_resistance:_aminoacids) <chr>,
## #   Amino_acid_range_(*:_partial_coverage_of_that_aminoacid) <chr>,
## #   pool5 <lgl>, amplicon_id <chr>, amplicon_start <dbl>, amplicon_end <dbl>,
## #   fwd_primer <chr>, rev_primer <chr>, n <dbl>
## [1] "List of samples that do not have >75% alleles with >100 reads, pool 5"
## # A tibble: 154 × 7
## # Groups:   sampleID [154]
##    sampleID                        pool  totreads   n50  n100 neg_control   norm
##    <chr>                           <chr>    <int> <int> <int> <lgl>        <dbl>
##  1 Gambia_Indie-1B_MH_1_AE_2023_0… 1B          86     0     0 FALSE       0     
##  2 Gambia_Indie-1B_MH_1_AE_2023_0… 1B         647     2     0 FALSE       0     
##  3 Gambia_Indie-1B_MH_1_AE_2023_0… 1B        3216    22    10 FALSE       0.227 
##  4 Gambia_Indie-1B_MH_1_AE_2023_0… 1B         138     0     0 FALSE       0     
##  5 Gambia_Indie-1B_MH_1_AE_2023_0… 1B         364     0     0 FALSE       0     
##  6 Gambia_Indie-1B_MH_1_AE_2023_0… 1B         862     2     0 FALSE       0     
##  7 Gambia_Indie-1B_MH_1_AE_2023_0… 1B        1550    14     3 FALSE       0.0682
##  8 Gambia_Indie-1B_MH_1_AE_2023_0… 1B        2037    18     5 FALSE       0.114 
##  9 Gambia_Indie-1B_MH_1_AE_2023_0… 1B        3295    24    15 FALSE       0.341 
## 10 Gambia_Indie-1B_MH_1_AE_2023_0… 1B         266     0     0 FALSE       0     
## # ℹ 144 more rows

Pool 2

## Rows: 31 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (10): locus-pool, Category, chr_malaria, GeneID, Gene, Reason to include...
## dbl  (4): ampInsert_start, ampInsert_end, amplicon_start, amplicon_end
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Create list of samples that fail any of the QC checks by pool

Reprep if <50% amplicons with >100 reads

Repool if >50% but <75% amplicons with >100 reads

## 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185300_PR1A5_S298 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185323_PR1A5_S218 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185326_PR1A5_S242 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185343_PR1A5_S264 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185391_PR1A5_S214 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185401_PR1A5_S216 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185567_PR1A5_S229 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185722_PR1A5_S250 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185876_PR1A5_S288 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185891_PR1A5_S276 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185903_PR1A5_S262 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185939_PR1A5_S274 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186025_PR1A5_S286 
##                                                        1 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186063_PR1A5_S300 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186076_PR1A5_S287 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186110_PR1A5_S240 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186138_PR1A5_S263 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186207_PR1A5_S241 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279974_PR1A5_S306 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279988_PR1A5_S293 
##                                                        1 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279991_PR1A5_S304 
##                                                        1 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279996_PR1A5_S255 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280016_PR1A5_S283 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280025_PR1A5_S284 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280046_PR1A5_S261 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280050_PR1A5_S224 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280052_PR1A5_S248 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280058_PR1A5_S303 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280081_PR1A5_S268 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280088_PR1A5_S285 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280106_PR1A5_S221 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280181_PR1A5_S295 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280188_PR1A5_S249 
##                                                        1 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280201_PR1A5_S256 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280279_PR1A5_S222 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280282_PR1A5_S236 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280290_PR1A5_S257 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280303_PR1A5_S246 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280304_PR1A5_S282 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280374_PR1A5_S266 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280398_PR1A5_S272 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280432_PR1A5_S260 
##                                                        2 
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280471_PR1A5_S225 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279954_PR1A5_S391 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279957_PR1A5_S370 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279962_PR1A5_S369 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279967_PR1A5_S380 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279976_PR1A5_S356 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279983_PR1A5_S335 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279990_PR1A5_S314 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279999_PR1A5_S403 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280004_PR1A5_S316 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280029_PR1A5_S317 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280043_PR1A5_S333 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280059_PR1A5_S321 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280060_PR1A5_S373 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280071_PR1A5_S358 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280080_PR1A5_S357 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280095_PR1A5_S332 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280117_PR1A5_S319 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280118_PR1A5_S382 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280144_PR1A5_S381 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280165_PR1A5_S343 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280195_PR1A5_S334 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280206_PR1A5_S350 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280213_PR1A5_S325 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280215_PR1A5_S384 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280218_PR1A5_S328 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280219_PR1A5_S383 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280224_PR1A5_S389 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280236_PR1A5_S312 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280243_PR1A5_S346 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280250_PR1A5_S401 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280252_PR1A5_S385 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280286_PR1A5_S344 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280296_PR1A5_S387 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280300_PR1A5_S348 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280312_PR1A5_S378 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280323_PR1A5_S386 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280325_PR1A5_S364 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280326_PR1A5_S400 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280411_PR1A5_S371 
##                                                        1 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280421_PR1A5_S374 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280430_PR1A5_S322 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280506_PR1A5_S399 
##                                                        2 
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280520_PR1A5_S331 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068279968_PR1A5_S449 
##                                                        1 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068279985_PR1A5_S441 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068279995_PR1A5_S429 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280003_PR1A5_S423 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280006_PR1A5_S434 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280007_PR1A5_S448 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280020_PR1A5_S499 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280045_PR1A5_S463 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280048_PR1A5_S442 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280074_PR1A5_S457 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280083_PR1A5_S415 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280090_PR1A5_S409 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280101_PR1A5_S446 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280104_PR1A5_S484 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280116_PR1A5_S435 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280124_PR1A5_S420 
##                                                        1 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280151_PR1A5_S493 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280159_PR1A5_S440 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280162_PR1A5_S410 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280164_PR1A5_S436 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280177_PR1A5_S462 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280184_PR1A5_S491 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280196_PR1A5_S458 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280203_PR1A5_S445 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280207_PR1A5_S468 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280231_PR1A5_S470 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280235_PR1A5_S424 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280239_PR1A5_S406 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280276_PR1A5_S492 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280283_PR1A5_S454 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280288_PR1A5_S456 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280298_PR1A5_S482 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280310_PR1A5_S426 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280315_PR1A5_S466 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280316_PR1A5_S479 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280320_PR1A5_S464 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280334_PR1A5_S467 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280346_PR1A5_S485 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280349_PR1A5_S407 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280351_PR1A5_S425 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280375_PR1A5_S418 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280393_PR1A5_S495 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280394_PR1A5_S431 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280396_PR1A5_S408 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280406_PR1A5_S497 
##                                                        1 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280409_PR1A5_S472 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280414_PR1A5_S432 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280429_PR1A5_S413 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280460_PR1A5_S444 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280469_PR1A5_S428 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280481_PR1A5_S476 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280485_PR1A5_S412 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280505_PR1A5_S447 
##                                                        2 
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280683_PR1A5_S477 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279948_PR1A5_S518 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279953_PR1A5_S516 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279965_PR1A5_S545 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279981_PR1A5_S558 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279993_PR1A5_S550 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280023_PR1A5_S551 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280027_PR1A5_S534 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280057_PR1A5_S541 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280126_PR1A5_S503 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280130_PR1A5_S528 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280134_PR1A5_S539 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280160_PR1A5_S519 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280211_PR1A5_S513 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280220_PR1A5_S530 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280225_PR1A5_S535 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280227_PR1A5_S557 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280237_PR1A5_S560 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280244_PR1A5_S548 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280292_PR1A5_S559 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280416_PR1A5_S537 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280419_PR1A5_S549 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280427_PR1A5_S556 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280440_PR1A5_S561 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280511_PR1A5_S538 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280512_PR1A5_S544 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280632_PR1A5_S527 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280637_PR1A5_S529 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280659_PR1A5_S536 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280666_PR1A5_S555 
##                                                        1 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280680_PR1A5_S552 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280685_PR1A5_S526 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280697_PR1A5_S531 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280711_PR1A5_S508 
##                                                        2 
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280715_PR1A5_S543 
##                                                        2
## Joining with `by = join_by(sampleID)`

Filtering

Remove bad samples

Remove bad loci

Remove controls

## [1] "Sample size= 151"
## [1] "# of entries excluded = 0, Prop. excluded = 0"
## [1] "# of loci after cleanup = 242"
## character(0)

Extra

rough MOI estimates (No. alleles per locus/ sample)

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

## `summarise()` has grouped output by 'locus'. You can override using the
## `.groups` argument.
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.